Hi,
Just here to say I have this same problem on both my laptop and desktop which share no common hardware, not even video card provider (1 is AMD, 1 is nVidia). There is no theming software installed on either PC. Curiously, this does not occur if mousing over a metro app's icon, so I think it...
I have the exact same problem. The same issue extends to the Alt-Tab windows as well, it pops under all of the open windows. It seems to have started with the new Windows 8.1 Update 1.
Edit: It's curious that it does NOT pop under metro apps so I think it may be caused by this new functionality...